Change the scale of the peptide intensity

Change the scale of the peptide intensity benoit fatou  2020-06-18

Hi Skyline Team,

I was wondering if it is possible to do a log2 transformation of the peptide intensities to then export the chromatogram as an image.
The idea is to uniform the intensity and make the chromatogram much nicer to visualize.


Brendan MacLean responded:  2020-06-18

Hi Benoit,
This is not possible and you are the first to request it. Though, it is simple enough for us to do that we might be able to add it in Skyline 20.2, if you post a TODO issue requesting it.

Dario Amodei, who implemented mProphet in Skyline and some of the Thermo demultiplexing used to present chromatograms with intensity on a log scale. I thought it was interesting, but he is the only person we have seen do that.

One thing Nick Shulman on the Skyline team has pointed out is that log scale y-axes can devote an inordinate amount of space to not very interesting values, e.g. 0 to 1 (0 to log = 0).

Generally, in Skyline we prefer to just use a log-scale y-axis rather than actually converting numbers to a particular log base (e.g. 2 as you requested or 10), and I am not a big fan of log 2 for intensity. Though it was pointed out to me that 10 log 2 is 1024 (so roughly 1000) at a May Institute on Statistical Proteomics at Northeastern. I tend to prefer log 10 for intensity and log 2 for fold-change.

Anyway, some things to be considered, but we would be willing to consider them, if you post a TODO issue in our Issues List.

Thanks for your feedback.